The results showed that haplotype A, which includes wild-type homozygous LMP2/TAP1 and mutant LMP7, decreases susceptibility to ESCC in the Kazakh population (OR = 0.37, 95%CI = 0.23–0.59, p<0.001), whereas haplotype E, which includes wild-type homozygous LMP2/LMP7/TAP1, acts as a risk factor to increase susceptibility to ESCC in the Kazakh population (OR = 3.67, 95% CI = 1.85–7.28, p<0.001). This evidence concerns the gene PSMB9 and esophageal squamous cell carcinoma.